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BALTIMORE — A federal judge on Monday declined to order the U.S. Naval Academy superintendent to recuse himself from deciding whether three midshipmen face a court-martial in a sexual assault case.

U.S. District Judge Ellen Hollander said she could not find precedent for a federal court to interfere with a pending investigation in military court.

“I think for me to stick my nose in the Navy’s business right now would be a far cry from appropriate,” Hollander said after hearing from the alleged victim’s attorney, Susan Burke, and counsel for academy head Vice Adm. Michael Miller.

Burke sought to have the court remove Miller from deciding whether the case of the three former football players, Tra’ves Bush, Josh Tate and Eric Graham, proceeds to a court-martial. She contends the superintendent is biased against her client because he thinks the case reflects badly on the academy and his leadership.

“He’s angry at the victim for speaking out,” Burke said.

Hollander noted that Burke went straight to federal court, without first seeking relief in the separate military system. The judge said Burke was asking the court to “micromanage the investigation.” She also said the request “trivializes the importance” of having a separate military justice system.

But Burke contended in the federal lawsuit that the superintendent “intentionally subverted the judicial process” to punish the alleged victim with abusive badgering from three legal defense teams over unreasonably long hours for days on the witness stand. She argued that the military court system has been hostile to her client, who is also a midshipman. She cited as an example her client’s experience in the courtroom during an Article 32 hearing that was held to help determine whether the case goes to a court-martial. It resembles a preliminary hearing in civilian court.

The Associated Press generally does not identify alleged victims of sexual assault.

Assistant U.S. Attorney Thomas Barnard, who is representing the superintendent, said that Miller is responsible for determining whether the case goes forward, and he would not preside over a court-martial.

“The bottom line is he’s not a judge,” Barnard said.

Barnard also said there is a higher convening authority over the superintendent who could review Miller’s decision. Barnard also said the superintendent would not have been given the authority to decide whether cases proceed to a court-martial, if it were believed he would be biased out of concern for the academy’s reputation.

Burke told reporters after the court hearing in Baltimore that she planned to pursue other legal options in military court. She noted that while the judge expressed her position from the bench and declined to issue a preliminary injunction to recuse the superintendent, she has not yet formally dismissed the federal lawsuit.

“We’re going to do everything,” Burke said.

The investigating officer in the Article 32 hearing, which ended early last month, has forwarded his recommendations to Miller, but the academy had declined to make the report public because the case is ongoing.

Bush and Tate are charged with aggravated sexual assault, while Graham is charged with abusive sexual contact in the case that came from an off-campus party in Annapolis in April 2012. The woman in the case initially did not want to pursue charges and testified last month that she has no memory of being assaulted and heard secondhand that she had sex with several people at the party.

Burke, an outspoken lawyer who has represented more than 200 sexual assault victims, has accused the academy of trying to sweep the case under the rug to protect its reputation.